[gmx-users] Re: query

[chiradip chatterjee]

HI friends
Thanks for your instant help. I got TFE
(trifluoroethanol) itp, pdb and gro files. Now I want
to disturb you again for a command. I have one TFE
molecule. I want to make a solvent box with 100 TFE
and 600 Water molecules. What are the commands to
translate this one TFE to 100TFE in a mixed solvent
box? [I found the water box filled with water in
share/tutor/water.]
Sorry to bother you, But it seems to be that you guys
are my teachers of GROMACS as I am just a 4 days old
baby in gromacs.
Chiradip

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> Paul van Maaren wrote:
> > On Sunday 12 November 2006 10:42, Tsjerk Wassenaar
> wrote:
> > 
> >> Probably someone will have a topology and a
> structure file for TFE
> >> lying around (not me). But TFE isn't the worst of
> molecules and since
> >> your new with Gromacs, I think it would be an
> excellent opportunity to
> >> get acquinted with the program and force fields
> by parameterizing it
> >> yourself. Find the paper of your favorite force
> field (choose one) and
> >> check how the parameterization of the building
> blocks / molecules was
> >> done. Take the same steps for TFE.
> >>
> >> Maybe this isn't the answer you'd hoped for, but
> think of the saying
> >> "give a man a fish and he can eat for a day;
> teach a man how to fish
> >> and..." :)
> > 
> > That's always a good approach, but for starters
> you might want to take a look 
> > at tfe.itp in the share/top directory.
> > 
> ... and check recent literature. IIRC there is a
> quite recent TFE model 
> for GROMOS-like force fields.
> 
> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 


Send instant messages to your online friends http://uk.messenger.yahoo.com